Difference between ZDoom and JDoom?

What gameplay features are different between ZDoom and JDoom?

jDoom doesn't have any special features, it can only run WAD's made to normal doom(2).exe. Only specials are the 3D models and dynamic lighting and stuff.
ZDoom has ACS scripting, like in Hexen, that makes many kinds of special effects possible, but it only has software rendering.
ZDoom also support's maps made for Boom engine, and it has much more editing possibilities.

There is also ZDoomGL, which is ZDoom (v1.22) renderd in OpenGL, but thats not exactly the most popular port due to its tendancy to crash upon loading up :/. Wait for the new one though, its looking really good...

I must say that few effects look better in ZdoomGL, so if your system can run it, get it also!

What about A3D or EAX sound effects?

JDoom has them, but my sound card doesn't support them so i don't know...